Quorum-based synchronization protocols for multimedia replicas

Multiple replicas of multimedia objects are distributed to peers in overlay networks. In quorum-based (QB) protocols, every replica may not be up-to-date and the up-to-date replica can be found in the version counter. Multimedia objects are characterized in terms of not only data structure but also quality of service (QoS) parameters like frame rate. A transaction reads a parameter of a replica while there is a type of read operation to read a whole state of a replica. Each parameter of a replica is changed through a write operation. Thus, the data structure and QoS parameters of a replica are independently manipulated. In the multimedia quorum-based (MQB) protocol, multiple replicas of a multimedia object are synchronized based on the newness precedent relation. An object is an encapsulation of data and abstract operations for manipulating the data. There are enriching and impoverishing types of write operations. Some data is added to a replica in an enriching operation. On the other hand, some data in a replica is removed in an impoverishing operation. In order to reduce the overhead to write every replica in a quorum, we take an approach that the state of each replica is not always updated. If a transaction issues an enriching write operation, every replica in the write quorum is updated in the same way as the QB protocol. On the other hand, if an impoverishing write operation is issued, every replica is not updated in the quorum. Impoverishing operations are just recorded in replicas. On receipt of a read operation to read a whole state, impoverishing operations recorded are performed on a replica. The MQB protocol is evaluated in terms of the processing overhead of replicas. We show that the processing overhead of each replica can be reduced in the MQB protocol.     

Preventing out-of-home placement for high-risk children

Preventing the removal of high-risk children from their families is investigated through two community-based programs. One program followed a day treatment model; the other used a home-based approach. These programs treated populations that shared common features but also had important differences. In both programs, a high percentage of children were maintained in the home and were still at home one year after discharge. It is suggested that such community-based intervention programs enhance the likelihood that high-risk children can remain with their families.     

An Effective Logical Cache for a Clustered LRC-Based DSM System

As local-area workstation networks are widely available, the idea of offering a software distributed shared memory (SDSM) system across interconnects of clusters is quite an attractive alternative for compute-intensive applications. However, the higher cost of sending a message over an inter-cluster link compared to an intra-cluster one can limit applications' performance on a multi-cluster SDSM system. In this paper, we present the extensions that we have added to the SDSM TreadMarks, which provides the lazy release consistency (LRC) memory model, in order to adapt it to a loosely-coupled cluster-based platform. We have implemented a logical per-cluster cache that exploits cluster locality. By accessing the cache of its cluster, a processor can share data previously requested by a second processor of its cluster, thereby, minimizing, the cost of inter-cluster communication.     

Ontologizing gene-expression microarray data: characterizing clusters with Gene Ontology

An XML-based Java application is described that provides a function-oriented overview of the results of cluster analysis of gene-expression microarray data based on Gene Ontology terms and associations. The application generates one HTML page with listings of the frequencies of explicit and implicit Gene Ontology annotations for each cluster, and separate, linked pages with listings of explicit annotations for each gene in a cluster.     

Aggregated Multicast – A Comparative Study

Though IP multicast is resource efficient in delivering data to a group of members simultaneously, it suffers from scalability problem with the number of concurrently active multicast groups because it requires a router to keep forwarding state for every multicast tree passing through it. To solve this state scalability problem, we proposed a scheme, called aggregated multicast. The key idea is that multiple groups are forced to share a single delivery tree. In our earlier work, we introduced the basic concept of aggregated multicast and presented some initial results to show that multicast state can be reduced. In this paper, we develop a more quantitative assessment of the cost/benefit trade-offs. We propose an algorithm to assign multicast groups to delivery trees with controllable cost and introduce metrics to measure multicast state and tree management overhead for multicast schemes. We then compare aggregated multicast with conventional multicast schemes, such as source specific tree scheme and shared tree scheme. Our extensive simulations show that aggregated multicast can achieve significant routing state and tree management overhead reduction while containing the expense of extra resources (bandwidth waste and tunnelling overhead). We conclude that aggregated multicast is a very cost-effective and promising direction for scalable transit domain multicast provisioning.     

TSGDB: a database system for tumor suppressor genes

A Web-based database system was constructed and implemented that contains 174 tumor suppressor genes. The database homepage was created to accommodate these genes in a pull-down window so that each gene can be viewed individually in a separate Web page. Information displayed on each page includes gene name, aliases, source organism, chromosome location, expression cells/tissues, gene structure, protein size, gene functions and major reference sources. Queries to the database can be conducted through a user-friendly interface, and query results are returned in the HTML format on dynamically generated web pages. AVAILABILITY: The database is available at http://www.cise.ufl.edu/~yy1/HTML-TSGDB/Homepage.html (data files also at http://www.patcar.org/Databases/Tumor_Suppressor_Genes)     

Priority based data gathering using multiple mobile sinks in cluster based UWSNs for oil pipeline leakage detection

Energy efficient and completely reliable data gathering in resource constrained sparse Underwater Wireless Sensor Networks (UWSNs) is challenging and requires dedicated routing techniques. Routing having mobility assistance employs a Mobile Sink (MS) or a mobile relay for data gathering. It mitigates transmission power consumption as well as relaying overhead. But multiple MSs should be deployed in order to reduce the load of a single MS. The visiting schedule of each MS should consider the priority of data, data gathering delay and buffer overflow of each sensor. In order to address these issues, a priority-based data gathering scheme using multiple MSs for clustered UWSN is proposed to help in pipeline leakage detection under the water. In this work, each MS is deployed in such a way so that it can move in both the directions i.e., top to bottom or bottom to top. When a Cluster Head (CH) receives critical data, it sends an emergency notification to the nearest MS via other CHs. Upon receiving the emergency notification, MS immediately visits that CH to gather the critical data (oil leakage).

     

Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval and resources that operate on the data in GenBank and a variety of other biological data made available through NCBI's Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing pages, GeneMap'99, Davis Human-Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP) pages, Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP) pages, SAGEmap, Online Mendelian Inheritance in Man (OMIM) and the Molecular Modeling Database (MMDB). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih. gov     

Web-Based Surveillance of Public Information Needs for Informing Preconception Interventions

Background

The risk of adverse pregnancy outcomes can be minimized through the adoption of healthy lifestyles before pregnancy by women of childbearing age. Initiatives for promotion of preconception health may be difficult to implement. Internet can be used to build tailored health interventions through identification of the public''s information needs. To this aim, we developed a semi-automatic web-based system for monitoring Google searches, web pages and activity on social networks, regarding preconception health.

Methods

Based on the American College of Obstetricians and Gynecologists guidelines and on the actual search behaviors of Italian Internet users, we defined a set of keywords targeting preconception care topics. Using these keywords, we analyzed the usage of Google search engine and identified web pages containing preconception care recommendations. We also monitored how the selected web pages were shared on social networks. We analyzed discrepancies between searched and published information and the sharing pattern of the topics.

Results

We identified 1,807 Google search queries which generated a total of 1,995,030 searches during the study period. Less than 10% of the reviewed pages contained preconception care information and in 42.8% information was consistent with ACOG guidelines. Facebook was the most used social network for sharing. Nutrition, Chronic Diseases and Infectious Diseases were the most published and searched topics. Regarding Genetic Risk and Folic Acid, a high search volume was not associated to a high web page production, while Medication pages were more frequently published than searched. Vaccinations elicited high sharing although web page production was low; this effect was quite variable in time.

Conclusion

Our study represent a resource to prioritize communication on specific topics on the web, to address misconceptions, and to tailor interventions to specific populations.     

A Bionic Approach for Topology Optimization for Tension-only or Compression-only Design

##正## A new bionic approach is presented to find the optimal topologies of a structure with tension-only or compression-onlymaterial based on bone remodelling theory.By traditional methods,the computational cost of topology optimization of thestructure is high due to material nonlinearity.To improve the efficiency of optimization,the reference-interval with material-replacement method is presented.In the method,firstly,the optimization process of a structure is considered as bone remodellingprocess under the same loading conditions.A reference interval of Strain Energy Density (SED),corresponding to thedead zone or lazy zone in bone mechanics,is adopted to control the update of the design variables.Secondly,a material-replacement scheme is used to simplify the Finite Element Analysis (FEA) of structure in optimization.In the operation ofmaterial-replacement,the original tension-only or compression-only material in design domain is replaced with a new isotropicmaterial and the Effective Strain Energy Density (ESED) of each element can be obtained.Finally,the update of design variablesis determined by comparing the local ESED and the current reference interval of SED,e.g.,the increment of a relativedensity is nonzero if the local ESED is out of the current reference interval.Numerical results validate the method.     

Detecting Memory and Structure in Human Navigation Patterns Using Markov Chain Models of Varying Order

One of the most frequently used models for understanding human navigation on the Web is the Markov chain model, where Web pages are represented as states and hyperlinks as probabilities of navigating from one page to another. Predominantly, human navigation on the Web has been thought to satisfy the memoryless Markov property stating that the next page a user visits only depends on her current page and not on previously visited ones. This idea has found its way in numerous applications such as Google''s PageRank algorithm and others. Recently, new studies suggested that human navigation may better be modeled using higher order Markov chain models, i.e., the next page depends on a longer history of past clicks. Yet, this finding is preliminary and does not account for the higher complexity of higher order Markov chain models which is why the memoryless model is still widely used. In this work we thoroughly present a diverse array of advanced inference methods for determining the appropriate Markov chain order. We highlight strengths and weaknesses of each method and apply them for investigating memory and structure of human navigation on the Web. Our experiments reveal that the complexity of higher order models grows faster than their utility, and thus we confirm that the memoryless model represents a quite practical model for human navigation on a page level. However, when we expand our analysis to a topical level, where we abstract away from specific page transitions to transitions between topics, we find that the memoryless assumption is violated and specific regularities can be observed. We report results from experiments with two types of navigational datasets (goal-oriented vs. free form) and observe interesting structural differences that make a strong argument for more contextual studies of human navigation in future work.     

Changing our package

Starting with Volume 7, Lethaia will use its pages better by introducing a two-column type area. The amount of text published without charges will remain the same as in preceding volumes, but any optional publication charges received or profit attained will be invested in more pages. To our- authors the new arrangement implies one simple but important change, namely adjustment of published figure size to the page width (140 mm) or column width (67.5 mm) whenever possible. New elements for bibliographic identification ( biblid ) are added to the cover, article-heads, and individual pages.     

A secure lossless recovery for medical images based on image encoding and data self-embedding

To protect the security of data outsourced to the cloud, the tampers detection and recovery for outsourced image have aroused the concern of people. A secure tampering detection and lossless recovery for medical images (MI) using permutation ordered binary (POB) number system is proposed. In the proposed scheme, the region of interest (ROI) of MI is first extracted, and then, ROI is divided into some no-overlapping blocks, and image encoding is conducted on these blocks based on the better compression performance of JPEG-LS for medical image. After that, the generated compression data by all the blocks are divided into high 4-bit and low 4-bit planes, and shuffling and combination are used to generate two plane images. Owing to the substantial redundancies space in the compressed data, the data of each plane are spread to the size of the original image. Lastly, authentication data of two bits is obtained for every pixel and inserted into the pixel itself within the each plane, and the corresponding 10-bit data is transformed into the POB value of 8-bit. Furthermore, encryption is implemented on the above image to produce two shares which can be outsourced to the cloud server. The users can detect tampered part and recover original image when they down load the shares from the cloud. Extensive experiments on some ordinary medical image and COVID-19 image datasets show that the proposed approach can locate the tampered parts within the MI, and the original MI can be recovered without any loss even if one of the shares are totally destroyed, or two shares are tampered at the ration not more than 50%. Some comparisons and analysis are given to show the better performance of the scheme.

     

Scalable and efficient workload hotspot detection in virtualized environment

Workload hotspot detection is a key component of virtual machine (VM) management in virtualized environment. One of its challenges is how to effectively collect the resource usage of VMs. Also, since data centers usually have hundreds or even thousands of nodes, workload hotspot detection must be able to handle a large amount of monitoring data. In this paper, we address these two challenges. We first present a novel approach to VM memory monitoring. This approach collects memory usage data by walking through the page tables of VMs and by checking the present bit of page table entry. Second, we present a MapReduce-based approach to efficiently analyze a large amount of resource usage data of VMs and nodes. Leveraging the power of parallelism and robustness of MapReduce can significantly accelerate the detection of hotspots. Extensive simulations have been performed to evaluate the proposed approaches. The simulation results show that our approach can achieve effective estimation of memory usage with low overhead and can quickly detect workload hotspots.     

Wikipedia as an encyclopaedia of life

In a 2003 essay E. O. Wilson outlined his vision for an “encyclopaedia of life” comprising “an electronic page for each species of organism on Earth”, each page containing “the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits.” Although biodiversity informatics has generated numerous online resources, including some directly inspired by Wilson’s essay (e.g., iSpecies and EOL), we are still some way from the goal of having available online all relevant information about a species, such as its taxonomy, evolutionary history, genomics, morphology, ecology, and behaviour. While the biodiversity community has been developing a plethora of databases, some with overlapping goals and duplicated content, Wikipedia has been slowly growing to the point where it now has over 100,000 pages on biological taxa. My goal in this essay is to explore the idea that, largely independent of the aims of biodiversity informatics and well-funded international efforts, Wikipedia has emerged as potentially the best platform for fulfilling E. O. Wilson’s vision.     

Accurate mass spectrometry based protein quantification via shared peptides

In mass spectrometry-based protein quantification, peptides that are shared across different protein sequences are often discarded as being uninformative with respect to each of the parent proteins. We investigate the use of shared peptides which are ubiquitous (~50% of peptides) in mass spectrometric data-sets for accurate protein identification and quantification. Different from existing approaches, we show how shared peptides can help compute the relative amounts of the proteins that contain them. Also, proteins with no unique peptide in the sample can still be analyzed for relative abundance. Our article uses shared peptides in protein quantification and makes use of combinatorial optimization to reduce the error in relative abundance measurements. We describe the topological and numerical properties required for robust estimates, and use them to improve our estimates for ill-conditioned systems. Extensive simulations validate our approach even in the presence of experimental error. We apply our method to a model of Arabidopsis thaliana root knot nematode infection, and investigate the differential role of several protein family members in mediating host response to the pathogen.     

Reducing the computational complexity of protein folding via fragment folding and assembly

Understanding, and ultimately predicting, how a 1-D protein chain reaches its native 3-D fold has been one of the most challenging problems during the last few decades. Data increasingly indicate that protein folding is a hierarchical process. Hence, the question arises as to whether we can use the hierarchical concept to reduce the practically intractable computational times. For such a scheme to work, the first step is to cut the protein sequence into fragments that form local minima on the polypeptide chain. The conformations of such fragments in solution are likely to be similar to those when the fragments are embedded in the native fold, although alternate conformations may be favored during the mutual stabilization in the combinatorial assembly process. Two elements are needed for such cutting: (1) a library of (clustered) fragments derived from known protein structures and (2) an assignment algorithm that selects optimal combinations to "cover" the protein sequence. The next two steps in hierarchical folding schemes, not addressed here, are the combinatorial assembly of the fragments and finally, optimization of the obtained conformations. Here, we address the first step in a hierarchical protein-folding scheme. The input is a target protein sequence and a library of fragments created by clustering building blocks that were generated by cutting all protein structures. The output is a set of cutout fragments. We briefly outline a graph theoretic algorithm that automatically assigns building blocks to the target sequence, and we describe a sample of the results we have obtained.     

Some correlations between development and respiration in the sand dollar egg,as shown by cyanide inhibition studies

Cyanide is a valuable tool for studying respiratory mechanisms and their r?le in embryonic development: it is relatively specific in its action, penetrates cell membranes readily, is active in low concentration, and may be controlled quantitatively (page 217). Echinarachnius is extremely sensitive to cyanide and the oxygen consumption of both eggs and of sperm is almost completely inhibited by 10(-5)M HCN (pages 219 and 221). Cell division is likewise arrested by the same concentration (page 223). One of the pronounced effects of an irreversible dosage of cyanide is the marked cytolysis or breakdown of the egg, both internally and at the cell membrane. This cytolysis appears to be related to the state of metabolism, and its occurrence varies with both the respiratory and developmental activity of the cell (page 224). The lethal dosage of cyanide varies with the state of development of the egg: the unfertilized egg is less susceptible than the fertilized one, and the susceptibility increases as the development of the fertilized egg proceeds (page 228). The Echinarachnius egg differs from that of Arbacia in respiratory behavior chiefly in its inability to survive prolonged anoxia: the sea urchin egg will tolerate for 24 hours a concentration of cyanide that kills the sand dollar eggs in 30 minutes (page 229). The Echinarachnius egg is apparently completely dependent upon cyanide-sensitive catalytic systems for its normal functioning and maintenance. Interference with this aerobic energy release mechanism results in irreversible damage to the egg (page 231).     

MUTbase: maintenance and analysis of distributed mutation databases

MOTIVATION: To develop tools for the submission of mutations to databases and maintenance of locus-specific mutation databases. Advanced, integrated computer systems are needed to store and organize the increasing mutation information. RESULTS: The MUTbase program suite provides an easy, interactive and quality-controlled submission of information to mutation databases. For further study of the databases on the World Wide Web, a number of tools are provided. The program package also writes and updates a large number of Web pages, e.g. about the distribution and statistics of disease-causing mutations, and changes in restriction patterns.     

Automatic discovery of sub-molecular sequence domains in multi-aligned sequences: a dynamic programming algorithm for multiple alignment segmentation

Automatic identification of sub-structures in multi-aligned sequences is of great importance for effective and objective structural/functional domain annotation, phylogenetic treeing and other molecular analyses. We present a segmentation algorithm that optimally partitions a given multi-alignment into a set of potentially biologically significant blocks, or segments. This algorithm applies dynamic programming and progressive optimization to the statistical profile of a multi-alignment in order to optimally demarcate relatively homogenous sub-regions. Using this algorithm, a large multi-alignment of eukaryotic 16S rRNA was analyzed. Three types of sequence patterns were identified automatically and efficiently: shared conserved domain; shared variable motif; and rare signature sequence. Results were consistent with the patterns identified through independent phylogenetic and structural approaches. This algorithm facilitates the automation of sequence-based molecular structural and evolutionary analyses through statistical modeling and high performance computation.